Does our sefer torah have an extra letter(s)?
Rashi in last week's parsha (Chayei Sarah) comments on the pasuk (25,6) ולבני הפילגשם that פילגשים is written חסר and therefore we learn out that Avraham only had 1 pilegesh Hagar. The only problem is that in our sifrei torah it is actually written ולבני הפילגשים with the extra י (and therefore the drasha is not valid). In other words either our sifrei torah have an extra letter or Rashi's is missing one.
This is not the only case either. R' Akiva Eiger (Shabbos 55a) collects over 20 cases from all over Shas, medrashim, etc. where our mesora differs from either Chazal's or the Rishonim.
The Beis Yosef (Yoreh Deah 275 at the end) quotes a Rashba who refers to this Rashi and says that if there is a conflict we go after the majority.
In short, while our mesora is very good it is not perfect and there are places where our sifrei torah are different then what Chazal and/or the Rishonim had.